Editorial

The Oxford English Dictionary dates the word 'genome' to 1926 but has not yet seen
fit to include the term 'epigenome' in its illustrious pages (where it would reside
handsomely between 'epigenist' and 'epigenous'). This differential treatment reflects
a state of affairs in which the epigenome has yet to infiltrate the popular imagination,
but belies the recent explosion of epigenomics in the scientific literature, where
as many as 70% of all abstracts featuring 'epigenome' have been published within the
last three years.

The present-day proliferation in epigenomics, in the exploration of the dynamic regulatory
layers that insulate the genome's static DNA sequence, has been enabled by novel high-throughput
techniques for interrogating the positioning of DNA (hydroxy)methylation, histone
marks and open chromatin. The ready availability of genomic data, without which we
could not map the location of these features, has provided the essential context needed
to make biological sense of the high-throughput data, and so propel epigenomics to
the forefront of mainstream biology.

In this special issue, Genome Biology presents a collection of articles that describe a diverse range of novel insights
into epigenomes, from human disease to ciliate reproduction to the containment of
endogenous retroviruses. We also include a number of methods that will improve and
simplify the study of epigenomics, in particular the computational steps that follow
data generation. Finally, a selection of review and comment articles give an overview
of current and future directions in epigenomics research.

A new software toolbox

The availability of new high-throughput methods creates a demand for software tools
to process and analyze the overwhelming flow of unintelligible raw data that will
inevitably be produced. Genome Biology has a proud history of publishing the most popular examples of such tools, with high
profile examples including Bowtie [1] (next-generation sequencing data), MACS [2] (ChIP-seq data) and DEseq [3] (RNA-seq data). The challenge of designing bioinformatics tools for the ever expanding
number of DNA methylation genome-wide profiling methods has been taken up by many
bioinformatics labs [4]. In the past few months, for example, Genome Biology has published SWAN [5], a method for reducing technical variation in data from the cutting-edge Illumina
HumanMethylation450 BeadChip platform, and Bis-SNP [6], a method for calling SNPs in bisulfite sequencing data, which also has the advantage
of improving the accuracy of methylation calls.

The special issue now adds a number of powerful new tools to assist those working
with DNA methylation data. BatMeth [7] is a mapper for Illumina and SOLiD bisulfite sequencing reads, and is faster and
more accurate than existing methods. BSmooth [8] takes your bisulfite sequencing data and tells you where the differentially methylated
regions are, even if the coverage of your reads is low. methylKit [9] is a suite of tools for the annotation and statistical analysis of DNA methylation
or hydroxymethylation data. EpiExplorer [10] is a webserver for super-fast epigenome browsing, interactive exploration and hypothesis
generation, with output transferrable to other tools, such as Galaxy and the Genome
HyperBrowser, for further analysis. The special issue even includes a new method for
cheaper, simpler and more high-throughput RRBS (reduced representation bisulfite sequencing)
[11], so we anticipate plenty more data being generated as inputs for these tools.

DNA methylation where it ought not be

The widespread presence of DNA methylation across the tree of life does have a few
notable exceptions: for example, the model nematode species Caenorhabditis elegans is a bona fide methylation-free zone. By extension, conventional thinking has held that DNA methylation
is missing throughout the nematode phylum. But researchers studying the nematode Trichinella spiralis now shatter this assumption as they describe, for the first time, the presence of
DNA methylation in the Nematoda phylum [12]. Unlike the free-living C. elegans, T. spiralis is a parasitic organism, and is notable as a widespread food-borne pathogen that poses
a problem in both human health and agriculture. T. spiralis belongs to a basal clade of Nematoda, having diverged from C. elegans several hundred million years ago in the late Precambrian [13], and so it seems possible that it has retained a DNA methylation machinery that may
have been present in the ancestral nematode.

DNA methylation in T. spiralis can readily be explained by the presence of a (previously unnoticed) putative DNA
methyltransferase in its genome, specifically a DNMT3 homolog - a gene that intriguingly has no known counterpart in any other nematode
[12]. But trickier to explain is the new report, also in this issue, of DNA methylation
in the ciliate Oxytricha trifallax, an organism that has no recognizable DNA methyltransferase [14].

The study in O. trifallax finds that methylation acts as a marker for sites of DNA elimination during the genome
rearrangement that is a signature feature of ciliated protist biology. Conversion
to hydroxymethylation is a key step in this process and, unlike the mysteriously missing
methyltransferase, putative homologs of the hydroxymethylation-generating Tet enzymes
can in fact be found in the O. trifallax genome [14].

If these stories of weird methylation have left you scratching your head, we include
a Research Highlight to explain the new findings in an easily digestible form, as
well as to place them in the context of existing work [15].

DNA methylation in human health: cause or correlation?

Changes in promoter methylation have frequently been reported in cancers, although
how these alterations relate to carcinogenesis is not clear. This special issue includes
a comprehensive analysis of CpG island methylation in the promoters of several human
cancers, from which it is concluded that hypermethylation occurs at sites already
repressed in pre-cancerous tissue, and so is not likely to be contributing to gene
silencing [16].

In addition to hypermethylation, hypomethylation at some promoters has also been associated
with cancer. Another study in this issue shows that the hypomethylation previously
observed in a rodent model of non-genotoxic carcinogenesis is the product of an active
demethylation mechanism that begins by converting methylation sites to hydroxymethylation
intermediates [17]. An accompanying Research Highlight argues for a new model of cancer epigenetics,
in light of recent revelations about hydroxymethylation [18].

Whether causative or correlative, promoter DNA methylation changes that are associated
with cancer can undoubtedly serve as useful biomarkers, as is demonstrated in an article
that successfully identifies prognostic methylation biomarkers from neuroblastoma
samples [19]. In the study, data from two genome-wide assaying methods were integrated with literature
mining to pinpoint the biomarkers, which were then validated using a methylation-specific
PCR assay [19].

Effective use of cancer DNA methylation biomarkers depends upon the availability of
tumor cell samples. For other diseases, it may be possible to test a more convenient
cell type, such as blood, where sampling of the affected tissue would be more invasive.
However, such a strategy relies on the assumption that the DNA methylation biomarker
in question is present across multiple tissues. A recent article in Genome Biology used matched brain and blood samples from the same individuals to show that some instances
of inter-individual variation in DNA methylation are replicated in both tissues [20]. An article in this issue now adds support to the hypothesis that blood tests may
give insight into DNA methylation changes in the brain [21]. In this case, the DNA methylation changes studied were those that are acquired during
the course of human aging, and included sites in the genome associated with early-onset
Alzheimer's disease [21].

Cancer and aging are far from the only areas of human health in which methylation
has been implicated, and this issue also explores DNA methylation in human heart failure.
In a perhaps surprising study, significant hypomethylation specific to satellite repeat
elements is reported, with hypomethylation events being accompanied by a strong upregulation
of the corresponding transcript [22]. Why one class of repetitive element in particular is implicated, with no significant
methylation changes observed in any other class, is an intriguing question.

Epigenome death match: endogenous retroviruses versus genes

The havoc that repeat elements are liable to wreak upon our genomes, as it seems may
sometimes be the case in human heart failure, is for the most part suppressed by DNA
hypermethylation. The authors of one article in this issue wondered whether any leakage
of DNA methylation from repeat elements into gene promoters might occur when a gene
is located in close proximity to a repeat sequence. In an examination of endogenous
retroviruses in mice, it was observed that, in most cases, the spreading of DNA methylation
was contained before it reached gene promoters [23]. How does the genome prevent these promoters from being hypermethylated? Evidence
is provided in the study for a defensive barrier formed by H3K4me3 and CTCF enrichment,
with H3K4me3 - typically representative of euchromatin - even encroaching into the
endogenous retrovirus element itself [23].

Every histone tells a story

Deciphering the genetic code was a task that occupied some of the world's sharpest
minds (and neck-tie designers [24]) for more than a decade, but understanding the instruction underlying each codon
has proved to be a far simpler task than unraveling the meaning of each histone modification.
A study in this issue uses ChIP-seq and mass spectrometry to characterize the histone
mark H2A.Z in mouse and human embryonic stem cells, as well as in neuronal progenitor
cells. The study clarifies the biology of a mark where previous work had reported
a confusingly diverse array of functions, and identifies a novel dually modified form
of H2A.Z, with both N-terminal acetylation and C-terminal ubiquitination [25].

Another research article in this issue focuses on H3K27me3, finding that this marker
of Polycomb-mediated gene silencing is associated with paralog divergence following
whole genome duplication in Arabidopsis [26]. The study is well complemented by a Review article on epialleles and plant evolution
[27] - epigenomics plays a particularly intriguing role in plants, given that their lack
of mobility relative to animals favors a potent epigenome capable of rapid responses
to environmental changes.

Future work on histones will be aided by CHANCE, a user-friendly software package
for assessing several different quality metrics in ChIP-seq data [28]. Obvious measures, such as the strength of the pull-down, form the core of CHANCE,
but handy extras include a facility to compare your data to that produced by the ENCODE
project, to see how well they match. CHANCE highlights the need for high quality ChIP-seq
data; happily, recent methodological innovations have dramatically improved the resolution
of this technique, as is highlighted in a Review article that also appears in this
issue [29].

Concluding remarks

Our special issue hopes to give a flavor, to both the experienced and the novice epigenomicist,
of the many exciting directions taken by contemporary research seeking to understand
and to exploit the epigenome. Genome Biology's editorial team would like to thank the many scientists who collectively responded
to our call for papers with a deluge of submissions, the many peer reviewers who -
as ever - have been generous with their time and intellectual creativity, and our
Guest Editor Dr Alexander Meissner, whose advice throughout his tenure has been invaluable
and who has kindly written his own Editorial as an alluring introduction to the epigenomics
field [30].